Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis

Wang, I-Chen; Lin, Hung‐Du; Liang, Chen-Jui; Huang, Chi‐Chun; Wang, Rong-Da; Jun, Yang; Wang, Wei-Kuang

doi:10.3897/zookeys.1005.57592

Cited by 13 publications

(14 citation statements)

References 29 publications

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“…The remarkable species P. progenetica of both samples (S3 and P1) from Peninsular Malaysia were aligned with 96% similarity of P. progenetica collected from Indonesia (AP011287) retrieved in GenBank entry. The overall nucleotide composition of P. progenetica was 33.0% A, 27.2% T, 23.5% C, and 15.5% G and showed a slightly AT-rich region (60.25%); these results were consistent with the patterns found in most fish mitogenomes [ 22 ]. The nucleotide composition of the P. progenetica mitogenome was highly biased toward A + T and had similar values as other Paedocypris species, such as P. progenetica from Banka.…”

Section: Resultssupporting

confidence: 83%

Characterization of the first mitogenomes of the smallest fish in the world, Paedocypris progenetica, from peat swamp of Peninsular Malaysia, Selangor, and Perak

et al. 2022

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The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.

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Section: Resultssupporting

confidence: 83%

Characterization of the first mitogenomes of the smallest fish in the world, Paedocypris progenetica, from peat swamp of Peninsular Malaysia, Selangor, and Perak

et al. 2022

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“…We compared the nucleotide composition of the mitogenomes of five Gobiobotia species, including two G. naktongensis populations (Table 2 ). The nucleotide composition of G. naktongensis Geum River was A = 30.3%, G = 16.8%, T = 26.3%, and C = 26.3%, showing a bias toward A + T (56.9%), similar to other Gobiobotia species, which is similar to the results of most fish mitogenomes (Wang et al 2020 ; Yang et al 2018 ).…”

Section: Resultssupporting

confidence: 82%

“…For example, H-strand encoded genes show a clear preference for C in the codon wobble position, whereas L-strand encoded genes for G or T. The PCGs of the mitogenome of G. naktongensis Geum River had a slightly higher AT content (56.9%) than the rRNA genes (55.2%) (Table 3 ). The control region, which occupies most of the non-coding region, showed a significantly higher AT content (66.5%), similar to the mitochondrial genes of other fishes (Wang et al 2020 ; Yang et al 2018 ; Zhou et al 2017 ). AT skews by gene regions were all positive, except for PCGs, and all GC skews were negative, except for tRNAs.…”

Section: Resultssupporting

confidence: 60%

Characterization of the complete mitogenome of the endangered freshwater fish Gobiobotia naktongensis from the Geum River in South Korea: evidence of stream connection with the Paleo-Huanghe

Kim

Kang

Kim³

et al. 2022

Genes Genom

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Background The freshwater fish Gobiobotia naktongensis (Teleostei, Cypriniformes, and Gobionidae) is an endangered class I species whose population size has been greatly reduced. Objective To successfully protect and restore the highly endangered freshwater fish G. naktongensis from the Geum River in South Korea. Methods The mitogenome was characterized using the primer walking method with phylogenetic relationships. Results The complete mitogenome of G. naktongensis Geum River was 16,607 bp, comprising 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA (tRNA) genes. Seventeen substitutions were found by comparing the tRNA regions between G. naktongensis Geum and Nakdong Rivers and G. pappenheimi; most were specific to G. naktongensis Nakdong River, with changes in their secondary structures. The comparison between G. naktongensis Geum River and G. pappenheimi revealed differences in the lengths of the D-loop and two tRNAs (tRNAArg and tRNATrp) and the secondary structures in the TΨC-arm of tRNAHis. In the phylogenetic tree, G. naktongensis Geum River did not cluster with its conspecific specimen from the Nakdong River in South Korea, but showed the closest relationship to G. pappenheimi in mainland China. Conclusions Our results support the existence of the Paleo-Huanghe River connecting the Korean peninsula and mainland China, suggesting that G. naktongensis in the Geum River should be treated as a different evolutionarily significant unit separated from that in the Nakdong River. The complete mitogenome of G. naktongensis Geum River provides essential baseline data to establish strategies for its conservation and restoration.

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“…The longest intergenic spacer was located between tRNA Asn and RNA Cys . These overlapping and intergenic regions are very common in fish mitochondrial genomes Wang et al 2020).…”

Section: Genome Organization and Nucleotide Compositionmentioning

confidence: 99%

The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications

Zhang¹,

Qian²,

Deng³

2021

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Mitochondria are important organelles with independent genetic material of eukaryotic organisms. In this study, we sequenced and analyzed the complete mitogenome of a small cyprinid fish, Microphysogobio elongatus (Yao & Yang, 1977). The mitogenome of M. elongatus is a typical circular molecule of 16,612 bp in length containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a 930 bp control region. The base composition of the M. elongatus mitogenome is 30.8% A, 26.1% T, 16.7% G, and 26.4% C. All PCGs used the standard ATG start codon with the exception of COI. Six PCGs terminate with complete stop codons, whereas seven PCGs (ND2, COII, ATPase 6, COIII, ND3, ND4, and Cyt b) terminate with incomplete (T or TA) stop codons. All tRNA genes exhibited typical cloverleaf secondary structures with the exception of tRNASer(AGY), for which the dihydrouridine arm forms a simple loop. The phylogenetic analysis divided the subfamily Gobioninae in three clades with relatively robust support, and that Microphysogobio is not a monophyletic group. The complete mitogenome of M. elongatus provides a valuable resource for future studies about molecular phylogeny and/or population genetics of Microphysogobio.

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Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis

Cited by 13 publications

References 29 publications

Characterization of the first mitogenomes of the smallest fish in the world, Paedocypris progenetica, from peat swamp of Peninsular Malaysia, Selangor, and Perak

Characterization of the first mitogenomes of the smallest fish in the world, Paedocypris progenetica, from peat swamp of Peninsular Malaysia, Selangor, and Perak

Characterization of the complete mitogenome of the endangered freshwater fish Gobiobotia naktongensis from the Geum River in South Korea: evidence of stream connection with the Paleo-Huanghe

The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications

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